But in 2008, the number of patients who came to the Mayo was flat. And more of them came with Medicare coverage.

At Mayo's campus in Rochester, 3 percent more of their patients were Medicare. Overall, the clinic lost $765 million on those patients.

Mayo's chief financial officer Jeff Bolton says that wasn't the only slip for the not-for-profit health care provider. Mayo lost 18 percent, or another $700 million, in investments.

"While there is really nothing very good you can say about an 18 percent loss for the year, on a relative basis when you compare it to industry benchmarks, it was favorable -- and actually by about 5 percentage points. The indices lost about 23 percent," said Bolton.

The pension plan took another hit. It is now $1.2 billion short of being fully funded.

And expenses ballooned. Mayo opened a new hospital in Florida, so expenses grew at 7.5 percent, while revenue grew at 4.5 percent.